SIRE1 retrotransposons in barley (Hordeum vulgare L.)

SIRE1 retrotransposons in barley (Hordeum vulgare L.)
Cakmak, B.; Marakli, S.; Gozukirmizi, N.
2015-07-25 00:00:00
Sireviruses are genera of copia LTR retrotransposons with a unique genome structure among retrotransposons. Barley (Hordeum vulgare L.) is an economically important plant. In this study, we used mature barley embryos, 10-day-old roots and 10-day-old leaves derived from the same barley plant to investigate SIRE1 retrotransposon movements by Inter-Retrotransposon Amplified Polymorphism (IRAP) technique. We found polymorphism rates between 0–64% among embryos, roots and leaves. Polymorphism rates were detected to be 0–27% among embryos, 8–60% among roots, and 11–50% among leaves. Polymorphisms were observed not only among the parts of different individuals, but also on the parts of the same plant (23–64%). The internal domains of SIRE1 (GAG, ENV and RT) were also analyzed in the embryos, roots and leaves. Analysis of band profiles showed no polymorphism for GAG, however, different band patterns were observed among samples for RT and ENV. The sequencing of SIRE1
GAG, ENV and RT domains revealed 79% similarity for GAG, 96% for ENV and 83% for RT to copia retrotransposons. Comparison between barley retrotransposons and SIRE1 in barley indicated that SIRE1-GAG, ENV and RT might be diverge earlier from barley retrotransposons. SIRE1 sequences were compared with SIRE1 in barley, results showed the closest homologues were SIRE1-ENV and SIRE1-RT sequences, and SIRE1-GAG sequences was a sister group to sequences of Glycine max. This study is the first detailed investigation of SIRE1 in barley genome. The obtained findings are expected to contribute to the comprehension of SIRE1 retrotransposon and its role in barley genome.
http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.pngRussian Journal of GeneticsSpringer Journalshttp://www.deepdyve.com/lp/springer-journals/sire1-retrotransposons-in-barley-hordeum-vulgare-l-5vZhRxWJfp

Abstract

Sireviruses are genera of copia LTR retrotransposons with a unique genome structure among retrotransposons. Barley (Hordeum vulgare L.) is an economically important plant. In this study, we used mature barley embryos, 10-day-old roots and 10-day-old leaves derived from the same barley plant to investigate SIRE1 retrotransposon movements by Inter-Retrotransposon Amplified Polymorphism (IRAP) technique. We found polymorphism rates between 0–64% among embryos, roots and leaves. Polymorphism rates were detected to be 0–27% among embryos, 8–60% among roots, and 11–50% among leaves. Polymorphisms were observed not only among the parts of different individuals, but also on the parts of the same plant (23–64%). The internal domains of SIRE1 (GAG, ENV and RT) were also analyzed in the embryos, roots and leaves. Analysis of band profiles showed no polymorphism for GAG, however, different band patterns were observed among samples for RT and ENV. The sequencing of SIRE1
GAG, ENV and RT domains revealed 79% similarity for GAG, 96% for ENV and 83% for RT to copia retrotransposons. Comparison between barley retrotransposons and SIRE1 in barley indicated that SIRE1-GAG, ENV and RT might be diverge earlier from barley retrotransposons. SIRE1 sequences were compared with SIRE1 in barley, results showed the closest homologues were SIRE1-ENV and SIRE1-RT sequences, and SIRE1-GAG sequences was a sister group to sequences of Glycine max. This study is the first detailed investigation of SIRE1 in barley genome. The obtained findings are expected to contribute to the comprehension of SIRE1 retrotransposon and its role in barley genome.

Journal

Russian Journal of Genetics
– Springer Journals

Published: Jul 25, 2015

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References

Plant retrotransposons

Kumar, A.; Bennetzen, J.L.

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